ODCurveToMetabolicGeneCurves: ODCurveToMetabolicGeneCurves

In CoRegFlux: CoRegFlux

Description

This function takes measured ODs and turn them into a ODcurveToMetCurve object to be visualize using visMetabolicGeneCurves(). It relies on flux variability analysis to highlight the flux value interval required to meet the specified OD and to map it on the metabolic genes.

Usage

ODCurveToMetabolicGeneCurves(times, ODs, metabolites_rates = NULL, model,
  softplusParam = 0, singlePointFluxEstimate = FALSE,
  biomass_flux_index = get_biomass_flux_position(model),
  aliases = NULL)

Arguments

times	A vector of timepoints at which the flux balance analysis solution will be evaluated.
ODs	vector of measured ODs.
metabolites_rates	A data.frame containing the extraneous metabolites, their initial concentrations and their uptake rates. Columns must be named "names","concentrations" and "rates".
model	An object of class modelOrg, the metabolic model.
softplusParam	Softplus parameter identify through calibration.
singlePointFluxEstimate	Optional, logical.
biomass_flux_index	index of the flux corresponding to the biomass reaction.
aliases	Optional. A data.frame containing the gene names used in the metabolic model and the aliases to use to match the regulatory network.

Value

Metabolic genes curves to visualize using the function visMetabolicGeneCurves

Examples

ODs<-c(0.4500000,0.5322392,0.6295079,0.7445529)
data("aliases_SC","iMM904")
ODcurveToMetCurve<-ODCurveToMetabolicGeneCurves(times = seq(0.5,2,by=0.5),
ODs = ODs,model = iMM904,aliases = aliases_SC)
visMetabolicGeneCurves(ODcurveToMetCurve,genes="YJR077C")

CoRegFlux documentation built on Nov. 8, 2020, 5:21 p.m.